How to Include Chromosome X in Your Genome‐Wide Association Study. Issue 2 (9th January 2014)

• Record Type: Journal Article
• Authors: König, Inke R.; Loley, Christina; Erdmann, Jeanette; Ziegler, Andreas
• Is Part Of: Genetic epidemiology. Volume 38:Issue 2(2014)
• Page Start: 97
• Page End: 103
• Publication Date: 2014-01-09
• Subjects: Genetic epidemiology -- Periodicals; Heredity -- Periodicals; Medical geography -- Periodicals; 614
• DOI: 10.1002/gepi.21782
• Languages: English
• ISSNs: 0741-0395

Abstract

<abstract abstract-type="main"> <title>ABSTRACT</title> <p>In current genome‐wide association studies (GWAS), the analysis is usually focused on autosomal variants only, and the sex chromosomes are often neglected. Recently, a number of technical hurdles have been described that add to a reluctance of including chromosome X in a GWAS, including complications in genotype calling, imputation, and selection of test statistics. To overcome this, we provide a "how to" guide for analyzing X chromosomal data within a standard GWAS. Following a general pipeline for GWAS, we highlight the steps in which the X chromosome requires specific attention, and we give tentative advice for each of these. Through this, we show that by selection of sensible algorithms and parameter settings, the inclusion of chromosome X in GWAS is manageable. Closing this gap is expected to further elucidate the genetic background of complex diseases, especially of those with sex‐specific features.</p> </abstract>